rs692607

Positions:

• chr11-50420232-T-C
• chr11-50420232-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024504.2(LOC646813):​n.435T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 1,076,986 control chromosomes in the GnomAD database, including 176,765 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.53 (22061 hom., cov: 32)
  • Exomes 𝑓: 0.57 (154704 hom.)
• Consequence: LOC646813 NR_024504.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.03

Genes affected

ENSG00000214883 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC646813	NR_024504.2	n.435T>C		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000214883	ENST00000532521.2	n.579T>C		non_coding_transcript_exon_variant	5/8	6

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79654 AN: 151310 Hom.: 22055 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.583

GnomAD4 exome AF: 0.575 AC: 531757 AN: 925558 Hom.: 154704 Cov.: 11 AF XY: 0.576 AC XY: 273150 AN XY: 474572

Gnomad4 AFR exome AF: 0.377

Gnomad4 AMR exome AF: 0.676

Gnomad4 ASJ exome AF: 0.678

Gnomad4 EAS exome AF: 0.543

Gnomad4 SAS exome AF: 0.560

Gnomad4 FIN exome AF: 0.581

Gnomad4 NFE exome AF: 0.575

Gnomad4 OTH exome AF: 0.575

GnomAD4 genome AF: 0.526 AC: 79685 AN: 151428 Hom.: 22061 Cov.: 32 AF XY: 0.528 AC XY: 39036 AN XY: 73966

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.588

Alfa AF: 0.544 Hom.: 3377

Bravo AF: 0.527

Asia WGS AF: 0.501 AC: 1744 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs692607; hg19: chr11-50379403;